Contacts of the helix formed by residues 394 - 417 (chain A) in PDB entry 2MBG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 4.2 9.4 - - - +
393A GLU* 1.3 82.8 + - + +
395A GLN* 1.3 65.5 + - - +
396A ALA* 3.4 2.0 - - - -
397A GLY* 3.8 17.4 - - - -
398A ILE* 3.0 27.7 + - - +
446A ALA* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLU 4.0 1.8 + - - -
394A THR* 1.3 72.4 - - - +
396A ALA* 1.3 58.9 + - - +
398A ILE* 3.2 4.0 + - - +
399A LYS* 2.9 45.6 + - + +
443A LEU* 2.9 45.3 + - - +
446A ALA* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A THR* 4.6 1.9 - - - -
395A GLN* 1.3 79.2 - - - +
397A GLY* 1.3 62.9 + - - +
399A LYS* 3.8 8.1 - - - +
400A GLU* 3.3 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 5.1 7.9 - - - +
394A THR* 3.3 21.3 + - - -
395A GLN 3.1 0.8 - - - -
396A ALA* 1.3 81.6 - - - +
398A ILE* 1.3 59.9 + - - +
400A GLU* 4.2 2.6 - - - +
401A GLU* 3.3 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 3.5 26.5 - - + +
393A GLU 4.7 1.8 - - - -
394A THR 3.0 20.5 + - - +
395A GLN* 3.2 4.7 + - - +
397A GLY* 1.3 77.4 - - - +
399A LYS* 1.3 56.4 + - - +
401A GLU* 4.5 3.4 - - - -
402A ILE* 2.8 64.5 + - + +
439A LEU* 3.5 28.7 - - + +
442A LYS* 3.6 37.7 - - + +
443A LEU* 3.9 9.4 - - + -
446A ALA* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLN* 2.9 43.7 + - + +
396A ALA* 3.8 8.5 - - - +
398A ILE* 1.3 78.2 - - - +
400A GLU* 1.3 69.5 + - - +
402A ILE* 3.5 3.5 + - - +
403A ARG* 3.2 20.3 + - - +
443A LEU* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA* 3.3 19.6 + - + +
397A GLY* 4.2 3.1 - - - +
399A LYS* 1.3 84.4 - - + +
401A GLU* 1.3 64.5 + - - +
403A ARG* 3.3 9.4 + - - +
404A ARG* 3.1 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN* 4.7 1.4 + - - -
377A MET* 3.1 34.6 - - + +
380A LEU* 6.5 1.6 - - + -
392A PRO* 5.9 6.3 - - + -
397A GLY* 3.3 20.4 + - - +
398A ILE* 3.3 4.9 + - - +
400A GLU* 1.3 76.6 - - - +
402A ILE* 1.3 54.4 + - - +
404A ARG* 2.6 40.6 + - - -
405A GLN* 2.7 34.0 + - - +
439A LEU* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 2.8 45.2 + - + +
399A LYS* 3.8 4.0 - - - +
401A GLU* 1.3 71.5 - - - +
403A ARG* 1.3 54.5 + - - +
406A GLU* 2.7 60.0 + - + +
436A LEU* 3.8 9.9 - - + -
439A LEU* 3.8 27.8 - - + +
440A LYS* 3.7 20.0 - - + -
443A LEU* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 6.1 1.6 - - - -
374A LYS* 6.1 1.0 - - - +
399A LYS 3.2 11.2 + - - +
400A GLU* 3.4 12.6 - - - +
402A ILE* 1.3 82.0 - - - +
404A ARG* 1.3 75.6 + - - +
406A GLU* 4.1 5.0 - - - +
407A PHE* 2.8 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 2.8 32.4 + - - +
222A LYS* 6.1 1.2 - - - +
375A GLN* 3.3 46.8 + - + +
376A VAL 5.4 2.5 - - - -
377A MET* 3.7 7.9 - - + +
400A GLU* 3.1 48.4 + - - +
401A GLU* 2.6 51.3 + - - +
403A ARG* 1.3 92.7 - - - +
405A GLN* 1.3 62.0 + - - +
407A PHE* 3.6 3.1 + - - +
408A LEU 3.3 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A MET* 3.4 28.9 - - + +
401A GLU* 2.7 19.7 + - - +
402A ILE 3.9 2.2 - - - +
404A ARG* 1.3 72.9 - - - +
406A GLU* 1.3 53.6 + - - +
408A LEU* 3.1 9.0 + - + +
409A LEU* 2.7 33.8 + - - +
432A VAL* 2.9 43.3 + - + +
435A ILE* 3.3 18.3 - - - +
436A LEU* 3.2 27.3 - - + +
439A LEU* 3.3 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 2.7 36.5 + - + +
403A ARG* 4.1 5.7 + - - +
405A GLN* 1.3 71.6 - - - +
407A PHE* 1.3 56.1 + - + +
409A LEU* 3.4 4.3 - - + +
410A ASN* 2.7 38.7 + - - +
436A LEU* 3.6 20.6 - - + +
440A LYS* 2.6 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 4.0 15.9 - - + -
403A ARG* 2.8 73.9 + - + +
404A ARG* 3.8 5.8 - - - +
405A GLN 3.2 0.2 - - - -
406A GLU* 1.3 75.2 - - + +
408A LEU* 1.3 63.3 + - - +
410A ASN* 2.6 27.7 + - - +
411A CYS* 3.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 3.5 34.1 - - + +
204A TYR* 3.6 24.6 - - + -
376A VAL* 6.2 0.2 - - + -
377A MET* 4.3 27.8 - - + +
404A ARG 3.3 10.2 + - - +
405A GLN* 3.1 9.7 + - + +
407A PHE* 1.3 78.8 - - - +
409A LEU* 1.3 57.6 + - - +
411A CYS* 4.9 1.3 - - - -
412A LEU* 2.8 52.6 + - + +
432A VAL* 4.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN 2.7 19.6 + - - +
406A GLU* 3.1 8.7 + - + +
408A LEU* 1.3 73.4 - - - +
410A ASN* 1.3 72.1 + - + +
412A LEU* 3.9 1.4 - - - +
413A HIS* 3.0 34.2 + - + +
429A LEU* 4.2 1.6 - - - +
432A VAL* 3.6 28.0 - - + -
433A GLN* 3.8 35.9 - - + +
436A LEU* 3.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU 2.7 22.2 + - - +
407A PHE* 2.6 46.8 + - - +
409A LEU* 1.3 82.3 - - + +
411A CYS* 1.3 68.6 + - - +
413A HIS* 3.9 4.5 - - - +
414A ARG* 2.8 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.4 27.4 - - + +
205A ASP* 4.0 20.2 - - - +
407A PHE 3.3 16.6 + - - +
408A LEU 4.1 2.2 - - - +
409A LEU 3.2 0.4 - - - -
410A ASN* 1.3 84.6 - - - +
412A LEU* 1.3 59.8 + - - +
414A ARG* 3.2 14.8 + - - +
415A ASP* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET 3.3 25.1 - - - +
204A TYR 3.9 11.2 - - - +
408A LEU* 2.8 43.8 + - + +
409A LEU* 4.0 2.9 - - - +
411A CYS* 1.3 73.7 - - - +
413A HIS* 1.3 67.3 + - - +
415A ASP* 3.2 23.3 - - + +
416A LEU* 3.7 10.4 + - - +
425A LYS* 5.6 17.4 - - - +
428A ARG* 5.0 22.2 - - + +
429A LEU* 4.2 10.5 - - + -
432A VAL* 5.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 3.0 23.2 + - + +
410A ASN* 3.9 6.7 - - - +
412A LEU* 1.3 78.5 - - - +
414A ARG* 1.3 55.3 + - - +
416A LEU* 3.3 9.0 + - + +
417A GLN* 2.8 47.6 + - - +
429A LEU* 3.5 35.3 - - + +
433A GLN* 3.7 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN* 2.8 55.0 + - - +
411A CYS* 3.2 13.9 + - - +
413A HIS* 1.3 77.3 - - - +
415A ASP* 1.3 66.5 + - - +
417A GLN* 2.9 31.6 + - + +
418A GLY 3.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A CYS* 2.9 13.6 + - - +
412A LEU* 3.2 17.5 - - + +
414A ARG* 1.3 76.9 - - - +
416A LEU* 1.3 65.4 + - - +
418A GLY* 3.0 13.3 + - - -
420A ILE* 3.3 39.4 - - - +
425A LYS* 2.6 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU 3.9 7.2 - - - +
413A HIS* 3.8 5.8 - - + +
414A ARG 3.2 0.8 - - - -
415A ASP* 1.3 78.7 - - - +
417A GLN* 1.3 72.0 + - - +
418A GLY 3.0 0.4 - - - -
419A GLY* 3.4 1.0 + - - -
420A ILE* 3.0 54.4 + - + +
421A LYS* 5.2 0.2 - - - -
422A ASP 4.7 2.2 - - - +
425A LYS* 3.8 29.2 - - + -
426A GLU* 4.2 24.9 - - + +
429A LEU* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A HIS* 2.8 48.0 + - - +
414A ARG* 2.9 25.2 + - + +
416A LEU* 1.3 84.4 - - - +
418A GLY* 1.3 55.5 + - - +
419A GLY 3.0 10.3 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il